Evidence map›Paper›PMID 33759124›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2021

Negative Image-Based Screening: Rigid Docking Using Cavity Information.

Pekka A Postila, Sami T Kurkinen, Olli T Pentikäinen

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Pekka A PostilaInstitute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, Turku, Finland.
Sami T KurkinenInstitute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, Turku, Finland.
Olli T PentikäinenInstitute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, Turku, Finland. olli.pentikainen@utu.fi.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Rational drug discovery relies heavily on molecular docking-based virtual screening, which samples flexibly the ligand binding poses against the target protein's structure. The upside of flexible docking is that the geometries of the generated docking poses are adjusted to match the residue alignment inside the target protein's ligand-binding pocket. The downside is that the flexible docking requires plenty of computing resources and, regardless, acquiring a decent level of enrichment typically demands further rescoring or post-processing. Negative image-based screening is a rigid docking technique that is ultrafast and computationally light but also effective as proven by vast benchmarking and screening experiments. In the NIB screening, the target protein cavity's shape/electrostatics is aligned and compared against ab initio-generated ligand 3D conformers. In this chapter, the NIB methodology is explained at the practical level and both its weaknesses and strengths are discussed candidly.

Indexed as

AlgorithmsBinding SitesCrystallography, X-RayCyclooxygenase 2Databases, ProteinDrug DiscoveryLigandsModels, MolecularMolecular ConformationMolecular Docking SimulationProtein BindingProteinsROC CurveSmall Molecule LibrariesSoftwareStatic ElectricityCyclooxygenase 2LigandsProteinsSmall Molecule LibrariesCavity detectionFlexible molecular dockingNegative image-based screening (NIB)Rigid molecular dockingVirtual screening

Identifiers

PMID33759124

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.